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Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BE8 PDB ENTRIES 3BE8 AND 1C4R experimental model PDB 1C4R PDB ENTRIES 3BE8 AND 1C4R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 8% PEG 20000, 0.1M MES PH6.5
Crystal Properties Matthews coefficient Solvent content 4.24 70.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.52 α = 90 b = 198.67 β = 90 c = 85.74 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2007-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.9 30 99.4 0.08 16.1 4.8 25251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4 99.9 0.56 3.3 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 3BE8 AND 1C4R 3.9 30 23955 1261 100 0.208 0.205 0.2122 0.276 0.2831 RANDOM 61.99
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 2.45 1.97 -4.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.618 r_dihedral_angle_3_deg 21.169 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_1_deg 8.921 r_angle_refined_deg 1.396 r_angle_other_deg 0.964 r_scangle_it 0.935 r_scbond_it 0.518 r_mcangle_it 0.505 r_mcbond_it 0.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.618 r_dihedral_angle_3_deg 21.169 r_dihedral_angle_4_deg 15.843 r_dihedral_angle_1_deg 8.921 r_angle_refined_deg 1.396 r_angle_other_deg 0.964 r_scangle_it 0.935 r_scbond_it 0.518 r_mcangle_it 0.505 r_mcbond_it 0.265 r_chiral_restr 0.081 r_mcbond_other 0.031 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11330 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing